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  <div class="section" id="rsoftpython">
<h1>RSoftPython<a class="headerlink" href="#rsoftpython" title="Permalink to this headline">¶</a></h1>
<p>RSoftPython is a set of python code meant to easily facilitate some
of the less computationally intensive proceedures of the RSoft project.
Eventually, we would like to wrap all of the C++ code in the RSoft
project and make it pythonic. In the meantime, the following sets of
code primarily allow a user to do four things:</p>
<ul class="simple">
<li><strong>Design your own structure functions</strong>:
In RSoftTools.RSoft, see OutputRSoftSF and the README on the RSoft
github page.</li>
<li><strong>Train and test hyperplanes</strong>:
In RSoftTools.RSoft, see OpenDynamicsI, OpenSFI, OpenPlaneO,
SelectTrainingSet, Train, WritePlane, CloseDynamicsI, CloseSFI,
ClosePlaneO, and the tutorial in the README on the RSoft github
page.</li>
<li><strong>Interact with structure functions directly</strong>:
In RSoftTools.RSoft, see OpenSFI, OpenSFO, CloseSFI, CloseSFO,
GetAngular, GetRadial, SetAngular, and SetRadial.</li>
<li><strong>Find distances between particles and construct neighbor lists</strong>
<strong>(slow)</strong>: In RSoftTools.MDTools, see DeltaR and GetNList. These
are particularly helpful when one has periodic boundary conditions.</li>
</ul>
<div class="section" id="rsofttools-classes">
<h2>RSoftTools Classes<a class="headerlink" href="#rsofttools-classes" title="Permalink to this headline">¶</a></h2>
<p>The following are classes within RSoftTools. They may be used by
invoking the commands ‘from RSoftTools import RSoft’ and
‘from RSoftTools import MDTools’.</p>
<table border="1" class="longtable docutils">
<colgroup>
<col width="10%" />
<col width="90%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft" title="RSoftTools.RSoft"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft</span></code></a>()</td>
<td>RSoft package for python.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.MDTools" title="RSoftTools.MDTools"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.MDTools</span></code></a>()</td>
<td>Molecular Dynamics Tools for python</td>
</tr>
</tbody>
</table>
</div>
<div class="section" id="rsoft-methods">
<h2>RSoft Methods<a class="headerlink" href="#rsoft-methods" title="Permalink to this headline">¶</a></h2>
<p>The following provides a list of functions that can be used on RSoft
objects.</p>
<table border="1" class="longtable docutils">
<colgroup>
<col width="10%" />
<col width="90%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.OpenDynamicsI" title="RSoftTools.RSoft.OpenDynamicsI"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.OpenDynamicsI</span></code></a>(nc_file_name,&nbsp;…)</td>
<td>Opens dynamic file in AMBER (netCDF) file format</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.OpenPlaneO" title="RSoftTools.RSoft.OpenPlaneO"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.OpenPlaneO</span></code></a>(nc_file_name)</td>
<td>Opens RSoftPlane file</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.OpenSFI" title="RSoftTools.RSoft.OpenSFI"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.OpenSFI</span></code></a>(nc_file_name)</td>
<td>Opens RSoftSF file</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.OpenSFO" title="RSoftTools.RSoft.OpenSFO"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.OpenSFO</span></code></a>(nc_file_name)</td>
<td>Opens RSoftSF file</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.CloseDynamicsI" title="RSoftTools.RSoft.CloseDynamicsI"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.CloseDynamicsI</span></code></a>()</td>
<td>CLoses input of AMBER NetCDF dynamics file</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.ClosePlaneO" title="RSoftTools.RSoft.ClosePlaneO"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.ClosePlaneO</span></code></a>()</td>
<td>Closes output of RSoftPlane file</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.CloseSFI" title="RSoftTools.RSoft.CloseSFI"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.CloseSFI</span></code></a>()</td>
<td>Closes input of RSoftSF file</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.CloseSFO" title="RSoftTools.RSoft.CloseSFO"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.CloseSFO</span></code></a>()</td>
<td>Closes output of RSoftSF</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.GetAngular" title="RSoftTools.RSoft.GetAngular"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.GetAngular</span></code></a>(f)</td>
<td>Gets angular structure functions</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.GetRadial" title="RSoftTools.RSoft.GetRadial"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.GetRadial</span></code></a>(f)</td>
<td>Gets radial structure functions</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.SetAngular" title="RSoftTools.RSoft.SetAngular"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.SetAngular</span></code></a>(f,&nbsp;SF)</td>
<td>Sets angular structure functions</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.SetRadial" title="RSoftTools.RSoft.SetRadial"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.SetRadial</span></code></a>(f,&nbsp;SF)</td>
<td>Sets radial structure functions</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.SelectTrainingSet" title="RSoftTools.RSoft.SelectTrainingSet"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.SelectTrainingSet</span></code></a>(…[,&nbsp;…])</td>
<td>Selects training set</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.Train" title="RSoftTools.RSoft.Train"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.Train</span></code></a>([n_eg,&nbsp;K,&nbsp;…])</td>
<td>Trains a softness hyperplane</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.WritePlane" title="RSoftTools.RSoft.WritePlane"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.WritePlane</span></code></a>()</td>
<td>Writes plane to RSoftPlane file</td>
</tr>
</tbody>
</table>
</div>
<div class="section" id="rsoft-attributes">
<h2>RSoft Attributes<a class="headerlink" href="#rsoft-attributes" title="Permalink to this headline">¶</a></h2>
<p>The following provides a list of attributes that can be used on RSoft
objects.</p>
<table border="1" class="longtable docutils">
<colgroup>
<col width="10%" />
<col width="90%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.etol_radial" title="RSoftTools.RSoft.etol_radial"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.etol_radial</span></code></a></td>
<td></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.mus" title="RSoftTools.RSoft.mus"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.mus</span></code></a></td>
<td></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.radial_Xs" title="RSoftTools.RSoft.radial_Xs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.radial_Xs</span></code></a></td>
<td></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.radial_Ys" title="RSoftTools.RSoft.radial_Ys"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.radial_Ys</span></code></a></td>
<td></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.etol_angular" title="RSoftTools.RSoft.etol_angular"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.etol_angular</span></code></a></td>
<td></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.xis" title="RSoftTools.RSoft.xis"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.xis</span></code></a></td>
<td></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.lambdas" title="RSoftTools.RSoft.lambdas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.lambdas</span></code></a></td>
<td></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.zetas" title="RSoftTools.RSoft.zetas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.zetas</span></code></a></td>
<td></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.angular_Xs" title="RSoftTools.RSoft.angular_Xs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.angular_Xs</span></code></a></td>
<td></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.angular_Ys" title="RSoftTools.RSoft.angular_Ys"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.angular_Ys</span></code></a></td>
<td></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.angular_Zs" title="RSoftTools.RSoft.angular_Zs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.angular_Zs</span></code></a></td>
<td></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.training_R" title="RSoftTools.RSoft.training_R"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.training_R</span></code></a></td>
<td></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.RSoft.training_NR" title="RSoftTools.RSoft.training_NR"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.RSoft.training_NR</span></code></a></td>
<td></td>
</tr>
</tbody>
</table>
</div>
<div class="section" id="mdtools-methods">
<h2>MDTools Methods<a class="headerlink" href="#mdtools-methods" title="Permalink to this headline">¶</a></h2>
<p>The following provides a list of functions that can be used on MDTool
objects.</p>
<table border="1" class="longtable docutils">
<colgroup>
<col width="10%" />
<col width="90%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.MDTools.DeltaR" title="RSoftTools.MDTools.DeltaR"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.MDTools.DeltaR</span></code></a>(rf,&nbsp;ri,&nbsp;bb,&nbsp;bc)</td>
<td>Difference between two vectors or sets of vectors</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="RSoftTools.html#RSoftTools.MDTools.GetNList" title="RSoftTools.MDTools.GetNList"><code class="xref py py-obj docutils literal notranslate"><span class="pre">RSoftTools.MDTools.GetNList</span></code></a>(pos_t,&nbsp;bb_t,&nbsp;bc,&nbsp;R_c)</td>
<td>Obtains a neighbor list for a set of particles</td>
</tr>
</tbody>
</table>
</div>
</div>


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  <h3><a href="index.html">Table of Contents</a></h3>
  <ul>
<li><a class="reference internal" href="#">RSoftPython</a><ul>
<li><a class="reference internal" href="#rsofttools-classes">RSoftTools Classes</a></li>
<li><a class="reference internal" href="#rsoft-methods">RSoft Methods</a></li>
<li><a class="reference internal" href="#rsoft-attributes">RSoft Attributes</a></li>
<li><a class="reference internal" href="#mdtools-methods">MDTools Methods</a></li>
</ul>
</li>
</ul>

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